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- PDB-3trd: Structure of an alpha-beta serine hydrolase homologue from Coxiel... -

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Basic information

Entry
Database: PDB / ID: 3trd
TitleStructure of an alpha-beta serine hydrolase homologue from Coxiella burnetii
ComponentsAlpha/beta hydrolaseAlpha/beta hydrolase superfamily
KeywordsHYDROLASE / Cellular processes
Function / homology
Function and homology information


Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Alpha/beta hydrolase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4947
Polymers23,1391
Non-polymers3546
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.861, 55.905, 62.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha/beta hydrolase / Alpha/beta hydrolase superfamily


Mass: 23139.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_1769 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83AV9
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate, 0.63M sodium dihydrogen phosphate, 0.94M dipotassium hydrogen phosphate, 0.02M sodium hydroxide, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 28889 / Num. obs: 28456 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.059 / Χ2: 0.872 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.5340.7413480.937195.1
1.53-1.554.40.62713780.804196.8
1.55-1.584.60.53813540.768197.1
1.58-1.624.70.45814030.785197.6
1.62-1.654.90.41113950.733198.2
1.65-1.694.90.34913870.789198.1
1.69-1.734.80.31914010.896197.9
1.73-1.784.90.26314120.802198.4
1.78-1.834.90.2213930.875198.2
1.83-1.894.90.18114110.97198.8
1.89-1.964.80.15114241.061199.4
1.96-2.044.90.10614320.841199.5
2.04-2.134.90.09514141.007199.6
2.13-2.2450.07514500.876199.9
2.24-2.385.10.05814520.807199.9
2.38-2.565.30.0514560.731100
2.56-2.825.30.04514470.8931100
2.82-3.235.40.03314740.8221100
3.23-4.075.20.02815021.03199.8
4.07-504.90.02515230.999195.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.256 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.886 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 1437 5.09 %RANDOM
Rwork0.1662 ---
all0.1679 30108 --
obs0.1679 28220 98.5 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.925 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso max: 61.66 Å2 / Biso mean: 17.5439 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.4543 Å20 Å2-0 Å2
2--2.9292 Å2-0 Å2
3----0.7345 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 20 269 1922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061691
X-RAY DIFFRACTIONf_angle_d0.9922295
X-RAY DIFFRACTIONf_chiral_restr0.068253
X-RAY DIFFRACTIONf_plane_restr0.005296
X-RAY DIFFRACTIONf_dihedral_angle_d13.235602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.55360.38521560.38972552270896
1.5536-1.61580.30891370.26662604274198
1.6158-1.68930.26521350.21312635277098
1.6893-1.77840.22331490.18992638278798
1.7784-1.88980.20741350.1632636277199
1.8898-2.03570.19751490.15452684283399
2.0357-2.24050.17561440.157227042848100
2.2405-2.56460.19581440.145727362880100
2.5646-3.23060.18781360.147727672903100
3.2306-31.26330.16941520.15142827297998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0132-0.00580.02060.03080.03090.14420.00490.01780.01360.0509-0.0134-0.0677-0.159-0.03290.00830.13960.008-0.02140.0909-0.01940.116917.095357.4998-5.9441
20.2624-0.1982-0.01160.1712-0.08340.1895-0.1797-0.20910.22560.18660.13010.0248-0.2022-0.0903-0.16690.14850.05740.02720.1679-0.03030.11738.196353.0841-5.5797
30.54750.07760.08730.57810.16310.2864-0.006-0.0039-0.0060.05180.0037-0.03420.014-0.005700.07390.0008-0.0040.0727-0.00250.071213.5344.3929-16.5611
40.0135-0.0037-0.020.01220.00980.06750.17720.0311-0.22970.05350.0467-0.10060.04050.08580.00440.1068-0.0008-0.01790.1309-0.02370.19737.593830.7335-29.2806
50.0560.03240.02180.04510.07080.06640.0156-0.0259-0.04870.08340.040.03890.035-0.033400.102-0.016-0.01220.1185-0.00680.10772.179239.874-25.5981
60.00920.0206-0.02970.09650.00950.1389-0.0250.0149-0.02440.0297-0.13790.26150.059-0.2904-0.11440.0967-0.00330.02360.1961-0.05850.1642-3.897144.3773-17.4637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ -2:13)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 14:28)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 29:162)A0
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 163:172)A0
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 173:192)A0
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 193:205)A0

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